Mutual exclusivity analysis of genetic and epigenetic drivers in melanoma identifies a link between p14ARF and retinoic acid receptor β signaling

Melanoma genomes contain thousands of alterations, including mutations, copy number alterations, structural aberrations and methylation changes. The bulk of this variation is stochastic and functionally neutral, with only a small minority representing "drivers" that contribute to the genesis and maintenance of tumors. Drivers are often directly or inversely correlated across tumors, reflecting the molecular and regulatory signaling pathways in which they operate. Here, we generated a profile of genetic and epigenetic drivers in 110 human melanoma cell lines and searched for non-random distribution patterns. We found statistically significant mutual exclusivity among components of each of the p16INK4A-CDK4-RB, RAS-RAF-MEK-ERK and PI3K-AKT pathways. In addition, we found an inverse correlation between promoter hypermethylation of RARB (encoding retinoic acid receptor β (RARβ)) and CDKN2A alterations affecting p14ARF (P < 0.0001), suggesting a functional link between RARβ signaling and the melanoma-suppressive activities of p14ARF. We show that all-trans retinoic acid (ATRA) can increase the expression of p14ARF in primary human melanocytes, and that the steady-state levels of p14ARF in these cells are regulated via RARβ. Furthermore, we show that the ability of ATRA to induce senescence is reduced in p14ARF-depleted melanocytes, and we provide proof-of-concept that ATRA can induce irreversible growth arrest in melanoma cells with an intact RARβ-p14ARF axis, independent of p16INK4A and p53 status. These data identify a previously unrecognized crosstalk between RARβ and p14ARF with possible implications for melanoma treatment, and highlight the power of mutual exclusivity analysis of cancer drivers to unravel molecular pathways.